Background: Previous evidence has suggested a strong association between school exclusion and health outcomes. However, as health risks are themselves related to the risk of experiencing a school exclusion, it has been challenging to determine the extent to which school exclusion impacts later health outcomes, as opposed to reflecting a marker for pre-existing risks. Aim: The aim of the current study was to address this challenge in estimating the medium-to-long-term impact of school exclusion of health and well-being outcomes. Methods: To this end, we used an inverse propensity weighting approach in the Next Steps data set (N = 6534, from wave 1, 2014, to wave 8, 2015). Results: We found that after weighting for propensity of treatment scores estimated based on a wide range of factors, including previous health indicators, there was a significant effect of school exclusion on a wide range of health and well-being outcomes. Discussion: These results provide some of the most robust evidence to date that school exclusion harms long-term health outcomes. Conclusion: The findings suggest that policies should aim to reduce exclusion and ensure access to preventative health support for those who experience a school exclusion.